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Bio::Index::Qual(3)   User Contributed Perl Documentation  Bio::Index::Qual(3)

NAME
       Bio::Index::Qual	- Interface for	indexing (multiple) fasta qual files

SYNOPSIS
	   # Complete code for making an index for several
	   # qual files
	   use Bio::Index::Qual;
	   use strict;

	   my $Index_File_Name = shift;
	   my $inx = Bio::Index::Qual->new(
	       '-filename' => $Index_File_Name,
	       '-write_flag' =>	1);
	   $inx->make_index(@ARGV);

	   # Print out several sequences present in the	index
	   # in	Qual format
	   use Bio::Index::Qual;
	   use strict;

	   my $Index_File_Name = shift;
	   my $inx = Bio::Index::Qual->new('-filename' => $Index_File_Name);
	   my $out = Bio::SeqIO->new('-format' => 'qual','-fh' => \*STDOUT);

	   foreach my $id (@ARGV) {
	       my $seq = $inx->fetch($id); # Returns Bio::Seq object
	       $out->write_seq($seq);
	   }

	   # or, alternatively
	   my $id;
	   my $seq = $inx->get_Seq_by_id($id); #identical to fetch

DESCRIPTION
       Inherits	functions for managing dbm files from Bio::Index::Abstract.pm,
       and provides the	basic funtionality for indexing	qual files, and
       retrieving the sequence from them. For best results 'use	strict'.

       Bio::Index::Qual	supports the Bio::DB::BioSeqI interface, meaning it
       can be used as a	Sequence database for other parts of bioperl

       Additional example code is available in scripts/index.

       Note that by default the	key for	the sequence will be the first
       continuous string after the '>' in the qual header. If you want to use
       a specific substring of the qual	header you must	use the	id_parser()
       method.

       You can also set	or customize the unique	key used to retrieve by
       writing your own	function and calling the id_parser() method.  For
       example:

	  $inx->id_parser(\&get_id);
	  # make the index
	  $inx->make_index($file_name);

	  # here is where the retrieval	key is specified
	  sub get_id {
	     my	$line =	shift;
	     $line =~ /^(\d+)/;
	     $1;
	  }

FEED_BACK
   Mailing Lists
       User feedback is	an integral part of the	evolution of this and other
       Bioperl modules.	Send your comments and suggestions preferably to one
       of the Bioperl mailing lists.  Your participation is much appreciated.

	 bioperl-l@bioperl.org			- General discussion
	 http://bioperl.org/wiki/Mailing_lists	- About	the mailing lists

   Support
       Please direct usage questions or	support	issues to the mailing list:

       bioperl-l@bioperl.org

       rather than to the module maintainer directly. Many experienced and
       reponsive experts will be able look at the problem and quickly address
       it. Please include a thorough description of the	problem	with code and
       data examples if	at all possible.

   Reporting Bugs
       Report bugs to the Bioperl bug tracking system to help us keep track
       the bugs	and their resolution.  Bug reports can be submitted via	the
       web:

	 https://github.com/bioperl/bioperl-live/issues

AUTHOR - James Gilbert,	Mark Johnson
       Email - jgrg@sanger.ac.uk, johnsonm-at-gmail-dot-com

APPENDIX
       The rest	of the documentation details each of the object	methods.
       Internal	methods	are usually preceded with a _

   _file_format
	Title	: _file_format
	Function: The file format for this package, which is needed
		  by the SeqIO system when reading the sequence.
	Returns	: 'qual'

   _index_file
	 Title	 : _index_file
	 Usage	 : $index->_index_file(	$file_name, $i )
	 Function: Specialist function to index	QUAL format files.
		   Is provided with a filename and an integer
		   by make_index in its	SUPER class.
	 Example :
	 Returns :
	 Args	 :

   id_parser
	 Title	 : id_parser
	 Usage	 : $index->id_parser( CODE )
	 Function: Stores or returns the code used by record_id	to
		   parse the ID	for record from	a string.  Useful
		   for (for instance) specifying a different
		   parser for different	flavours of Qual file.
		   Returns \&default_id_parser (see below) if not
		   set.	If you supply your own id_parser
		   subroutine, then it should expect a qual
		   description line.  An entry will be added to
		   the index for each string in	the list returned.
	 Example : $index->id_parser( \&my_id_parser )
	 Returns : ref to CODE if called without arguments
	 Args	 : CODE

   default_id_parser
	 Title	 : default_id_parser
	 Usage	 : $id = default_id_parser( $header )
	 Function: The default Qual ID parser for Qual.pm
		   Returns $1 from applying the	regexp /^>\s*(\S+)/
		   to $header.
	 Returns : ID string
	 Args	 : a qual header line string

perl v5.32.0			  2019-12-07		   Bio::Index::Qual(3)

NAME | SYNOPSIS | DESCRIPTION | FEED_BACK | AUTHOR - James Gilbert, Mark Johnson | APPENDIX

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